Dying Embers
by Kyouryoku Senshi
Summary: Post My Struggle II. What deal exactly did Monica Reyes make with CSM?  What happened to Mulder & Scully? And whatever happened to Doggett?
1. Chapter 1

Title: My Choice

Author: KS

Rating: PG-13

Spoilers: My Struggle II

Summary: Post My Struggle II. What deal exactly did Monica Reyes make with CSM? What happened to Mulder & Scully? And what became of John Doggett?

Disclaimer: Everything belongs to Fox, 1013 and Chris Carter. I'm just picking up where they left off. :)

John Doggett heard a soft knock on his door and sighed when he saw none other than Monica Reyes. He never agreed with her choice to work for CSM when he came to her not long after Mulder's trial. He was angry that she would sacrifice everything she believed in to do his dirty work. But immunity to everything that was happening now wasn't the only reason she had agreed to it.

Monica had told him that the Cigarette Man knew where William was and threatened to expose his whereabouts if she didn't comply with his request. In fact, when she initially declined, calling his bluff...he showed just how serious he was by killing William's adoptive parents. This was about 3 years after Mulder's trial. John and Monica, still at the FBI, had found William and had taken him in to care for themselves.

At the expense of William and their now 12 year old daughter...Monica had reluctantly agreed to trade her life's work at the FBI for immunity for herself and her family...even if she couldn't always be with them. John still worked with local law enforcement, but due to Monica's dealings with CSM, he had to resign from the FBI as well.

John looked at Monica's somber expression as she stood in the doorway. It had felt like it had been forever seeing seeing her again...even though it had only been just a few months. "Monica."

She pushed past him into the small house that they had once called their own. "John, I'm sorry, but I don't have much time."

Even though part of him resented her for not exposing CSM, he still loved the fact that she had made this choice to protect them all.

He had just been watching the terror on the news about global contagion and out break. He hadn't left the house at her request...even though years ago she had given him and their daughter, Alexis, a vaccine that would protect them against the out break.

He watched the look on her face. "I saw Dana today...I told her...I warned her about everything that's happening right now."

Doggett sighed. He hadn't seen Dana or Mulder in about 14 years since Mulder escaped his trial. When he heard they had returned to the FBI a few weeks ago from Monica, he resisted the urge to meet with them as well.

John said nothing as he watched her. "You didn't tell her about-"

"No, I didn't. I couldn't. I wanted to. She thinks I am a coward for doing what I did."

John signed. "What are you doing here then, Monica? Won't he know if you're gone?"

Monica swallowed before she continued to say what she said next.

"Mulder is sick, near death. He offered Mulder the vaccine too...for a cost, but he refused. I can't say I blame him."

John sighed. "Then what?"

Monica swallowed. "There is another way."

"What, Monica?"

Monica looked up as a tall teenaged boy with blue eyes walked into the room...as if sensing their conversation.

"Aunt Monica...Uncle John."

"William," Monica sighed.

"They're in danger aren't they...my mom and my dad."

Monica simply nodded. John turned from her to face William.

"I can help them, can't I?"

"Yes, I believe you can, but it's dangerous."

"Will, don't go," begged the girl he had come to know as his sister. She was about 4 and he was about 7 when he came to live with them. She was the one who comforted him as he dealt with the death of adoptive parents and told him it was going to be okay.

He turned to the pre-teen who had dark hair and blueish-green eyes. "Don't worry, Lexi. I'll be fine. We both will."

John nodded reluctantly. "Okay son, but let one of us go with you."

Will shook his head. "No, my grandfather will hurt both of you. You've already changed your lives so much to raise me. Let me protect you."

John smiled. He definitely was insistent on his ways like his biological father. He was more than happy to raise William as his own. It was only fairly recently he had been able to let go of the guilt he harbored over Luke's death. It was always one of the major forces between he and Monica. Another thing that had kept them at a distance from one another. Until Luke had come to him in a dream...telling him to let him go. Much like the way Dana Scully had once told him in confidence about the daughter she lost. In a way, he adopted William not only for his sake and for Mulder & Scully's sake...but so he would be able to make amends in a way for not being able to raise Luke.

William sensed his Uncle's reluctance. "I know you worry about me, Uncle John...but I have to do this. I need to meet my biological parents and protect all of you."

Monica and John had still very reluctantly agreed. Even though it wasn't safe, this was what he needed to do. He needed to finally see his parents after all these years.

A/N: I need to resolve the revival ending for my own sanity and get some things answered. Hope you guys like this so far.

To be continued...


	2. Chapter 2

Scully felt as if her body had turned into cement as she stirred. She felt herself pressed hard against the concrete...straining against the nearly suffocating silence. It was then she remembered a bright light from a ship coming towards her and Agent Miller. She nearly jumped up as if the dead weight was suddenly lifted. The quiet around her amidst the terrain of cars sent chills down her spine. She saw Agent Miller on the ground next to her and quickly checked for a pulse. It was faint, but he was alive. She scrambled to put one of the IV packs which lay on the cement in his arm. He moaned. "Agent Scully...Mulder."

She gasped. Nearly stricken that she had forgotten about a near death Mulder in the car. How could she forget that? Guilt ridden, she grabbed the last IV pack with the vaccine and threw open the door. "Mulder," she yelled desperately.

She felt as if her heart had been ripped from her chest and thrown to the floor. His eyes were closed and she checked his pulse. As she did so, she felt her blood run cold as reality started to sink in. How long had she been out? Why didn't she put the damned IV in before wasting time telling Agent Miller that it might not work?! "Oh god, Mulder...no. Please," she started to sob as her trembling fingers felt their way up his stone cold arm...shaking so much that she had great difficulty getting the IV in.

"Mulder, wake up please, I'm here. Please wake up."

She did her best to perform quick CPR to no avail. He was completely unresponsive. She felt herself hit her head in frustration against the top of the car. "God, it's all my fault. Why did I wait so long?!"

She should have noticed the deafening silence around her, but all she could focus on was how she had manage to lose him, again. She fell to her knees and held onto him tightly. "I'm so sorry, Mulder. For not getting to you on time. For leaving. For everything. I was afraid. I was a coward."

"I lied, it wasn't because of your depression that I left. It was because I couldn't live with myself anymore...with everything that's happened. I wanted, needed someone else to blame. I'm the reason for all of this. I couldn't get to you on time and I gave up your last chance of survival when I gave our child up for adoption."

She felt herself holding onto him tightly for dear life as she felt her body shape violently between sobs. "You were all that I had left and I gave up. I'm so sorry, Mulder. If you could just open your eyes...I would do anything. I would come home to you and never leave again. Please."

She sat in that awkward position for what seemed like an eternity before what happened next shoot her from her stupor.

"Scully."

She looked up and gasped, letting a few more tears loose. He gingerly reached his free arm up to run his fingers through the waves of her strawberry blonde hair. He had been wanting to do that for some time and she finally let him after all these years.

"What you said, don't forget I'm going to hold you to that," he smirked.

She managed a heavy laugh. "Oh god, I guess you got me there."

Jeeze, how long was he listening for before he decided to say something? She looked over at the IV in his other arm. It seemed to be working, though she doubted for now long.

"Please don't tell me it was all to get me to wake up," he muttered.

"No, I meant that Mulder. I did...I do."

She took in his breath as he started to close his eyes. "Mulder, stay with me, okay? I need to get you out of here."

"Scully," he muttered as she fumbled with her phone. "Bright light," he continued. "Took you away."

That stopped her short as she looked at him earnestly. "No, I'm right here, Mulder. It didn't take me away. They didn't take me."

"They took you, Scully."

"Mulder, you're just delirious," she insisted more for herself than anything else.

"No, Scully. You were gone. Ship took you...you were gone for a while."

Scully did recall the light that focused down on her and the dire fear she felt of being abducted again. But she was here. They didn't take her, they couldn't have.

"Mulder, if they took me, we wouldn't be here talking."

"You don't...believe me."

Her heart sank. The whole reason we went on his little escapade despite being so sick was for this very reason. He still thought she didn't trust his judgement. She wished she could kick herself for making accusations at him for endogenous depression. As a doctor she knew they were too close for her to properly make that diagnosis. He had resented her for that.

He sighed and closed his eyes once more. It was that moment that she noted the eerie silence. She struggled to get her legs to cooperate and used the car door to pull herself back to hear feet.

Something wasn't right. The whole bridge was bathed in utter silence. Everything was black and absolutely still. Was this really the end. She swallowed back tears as she looked back towards Mulder and Miller. They both needed to get to a hospital, but there was no way to get them out of this gridlocked bridge on foot.

And what of Mulder. She was certain her treatment wouldn't work. He had been sick for God knows how long and more than likely suffering organ damage, to which extent she couldn't tell. She looked down at her cell phone, which read "No Service". All of the infrastructures had fallen, so this shouldn't have been any surprise. But she couldn't dare give up hope.

"Dana, I know where William is," Monica's voice echoed in her head. "They killed his adoptive parents after I told the cigarette man initially that I wouldn't cooperate."

Scully fought back tears as she recalled the sting of Monica's words that she had been working for CSM all these years. She wasn't sure if it was that fact or the fact that he was somehow still alive that stung her the most. "Three years after he came to me, I agreed to do his dirty work...but I had a condition of my own."

"Monica, you still haven't told me something. Where is Agent Doggett? He's been gone from the FBI nearly as long as you."

Monica swallowed. "Agent Doggett is with William...somewhere safe. That was the condition that we had."

Scully closed her eyes. She couldn't dare ask her next question. All these years, she had wondered where her son was...if he was safe or happy. He had been with John and Monica this entire time? As much as she wanted to see William or go to him in that moment, she knew that doing so would have only jeopardized his and Monica's lives.

But now, looking down at her useless smartphone, she felt the tears start to fall. Her strawberry blond locks falling into place around her face. He was Mulder's only chance of surviving this and maybe everyone else as well.

After all these years, she didn't want their sacrifices to be all for nothing. She wanted Mulder to be able to see the child he hasn't seen since he was just a few days old. Even if it was only for a moment.

A sudden movement in the deafening brought her out of her reverie. She glanced around in every direction. Suddenly, amidst all the gridlock, she could see a figure coming in their direction. As it got closer, she stumbled, bracing herself on the roof of the car. Panic and anticipation filled her at the same time. It was a man, no a boy...a teenager. He was tall, but felt oddly familiar. "Oh, God." That was the last thing she could recall before her knees his the cement and the world seem to collide around her.

To be continued...


	3. Chapter 3

Will sat next to his mother, watching over her carefully as she rested. The ship had taken them as he knew they would and they had taken his dad away. To do what or where, he wasn't sure. But he knew he needed to help him. He was dying. He knew it was his evil grandfather that Aunt Monica always talked about. He had seen him a few times since she was forced to work for him for a long time. He felt sad for Aunt Monica and Uncle John...and his cousin Alexis...though she always referred to her as his sister. She was always there for him. She made him feel safe when he first came to be with Aunt Monica and Uncle John. He worried about them still when he left. He wanted to protect them, but he knew he had to protect his mom and dad too. They needed his help. When he first saw his mother on the bridge, he knew that she knew who he was. She had fainted by the time he had reached them and the bright light came.

He didn't want to wake his mother. His grandfather told him she would be that way for a while. He watched over her as she slept peacefully. She was much like the mother he remembered in his dreams who always came to comfort him when he cried as a baby. Beautiful red hair, even though it had lightened considerably over the years. Porcelain skin that started to show the markings of age. But she was still beautiful.

He gently reached out and gripped her wrist. His Aunt Monica had always told him how much his mother loved him and how difficult it was for her to watch her give him away. But she always said his mother loved him so much and wanted to keep him safe. Even if she couldn't be with him. He never questioned that. He always had vivid dreams from his early memories of a newborn. He knew he was different. No other kids he knew had memories like that. He always remembered his mother being sad and it had never failed to make him depressed. Was he the reason? Aunt Monica would tell him it was because she was afraid some bad people would come to hurt him. He believed her. Aunt Monica was in a lot of the dreams too, comforting his mom. One of the times, his Uncle Jeffery had injected him with something that would keep the bad guys from finding him. Remembered his mom being afraid something bad had happened to him. Looking at her now, stress clearly evident in cause of age, he wanted to tell her that he wasn't upset with her.

He felt her move slightly under his touch. "Will," she whispered.

"It's okay, mom...I'm here."

Her eyes remained unopened and he knew she wasn't aware of his presence. She relaxed slightly though under his grip. He wanted so much for those arms to hold him and comfort him like they used to.

He tensed as he saw tears begin to fall down her cheeks. "William...our son, I gave him up...our son," she kept repeating.

His mother was having a nightmare and there was nothing her could do. "It's okay mom. It's okay," he tried, rubbing her arm.

His mother was small, like he had seen in photos. In his dreams, she was fiercely protective over him...she always made him feel safe. It wasn't until now that he realized how fragile she was. He hoped she would wake up soon.

To be continued...


	4. Chapter 4

Mulder had awoken to the smell of a newly lit cigarette that was all too familiar. He could say where he was, but he felt himself in a blanket of white. Was this what death was and going to heaven was like?

His temple throbbed and the last thing he could remember was being at death's doorstep. He groaned. The back of his eyelids burned fiercely from sickness and exhaustion. He swore he left that cigarette smoking sonofabitch's home.

"What's the matter, Fox?"

"What the hell are you doing here. I don't want you help and I don't need your pity. Go away."

"Should have accepted my offer, Fox. Agent Reyes did. She even went and gave this news to Scully...as I knew she would. It's how your beloved when on a rampage to find a cure. Even tried to create a vaccine using her own alien DNA, it's why we had to stop her. She even tried to save you...but you're too far gone, Fox. No one can save you now."

"What did you do to her?" he demanded angrily. Was he really dead? He did recall Scully coming to him, saying she was going to put an IV in him and then whispering to Miller something about stem cells. Then there was that bright light. In that moment, he couldn't care less what was happening to him if he was really at death's door right now. But Scully deserved none of this. All he wanted was to go back and relive the previous week, where he and Scully had reconciled after all that time apart. Things were finally back in place for them. Now, poof! All gone.

He winced.

"Don't worry, no harm has come to her, yet."

"Why do you think Monica traded her life for this, Fox? Did you think it was just simple devotion for Scully? Though I'm sure that is a big part of it."

"Because knowing you, you sick sadistic son of a bitch manipulated her like a pawn in your little game," Mulder muttered.

Spender chuckled, his son's anger and hatred for him never ceased to amuse him. He flicked away a cigarette butt. "What if I told you that she found out that little boy was her nephew."

Mulder laughed incredulously.

"What, you think this is a joke?"

"The only joke is in front of me right now."

"Did you know Agent Reyes was adopted, Fox?"

"So are a million other people on this planet."

"I swear, I never met someone who reminded me so much of you until I met her. She was the same way when I told her about my offer. Still is...defiant, rebellious."

"Cut the bullshit."

"What if I told you Monica was your sister, Fox? The sister you've been looking for a all these years, in all the wrong places."

Mulder's mind flashed back to a conversation he had with Scully not long ago. "This is about you saving your sister," a slightly younger, longer haired and distressed Scully called to him in the coldest of nights. "My sister is dead."

"That hasn't stopped you from looking for her."

He closed his eyes and sighed.

"My sister is dead. I saw her. She came to me."

"What you saw was your mind playing tricks on you, Fox. That is what we wanted you to believe. So you would give up searching for her."

Mulder lunged at him, angrily...wishing he hadn't left his gun in the man's house. "That's impossible. Why should I believe you?"

Mulder slapped his hand away as he reached for another cigarette.

"Well, you have every reason not to. But I think we both know you don't have the luxury not to believe me."

Mulder, fell to his knees and closed his eyes. "So you planned this. Her coming to the FBI, all of it."

"No, in fact, she had no clue. She didn't even even have any memories before eight. Although when I told her ten years ago, you might imagine the shock."

"Lying piece of shit."

"She uttered similar verbiage, Fox."

"This plague you infected everyone with. She's not affected."

"That was part of the deal...I make her immune, along with Agent Doggett and their daughter...your niece."

Mulder closed his eyes. He could feel the burning behind them. All this time, he had been led to believe he had no family left. Nothing, but Scully...of course.

"Tell me about her."

"Your niece? I would be happy to, Fox. This girl is about 12 years old...she was raised together with William after his adoptive family was killed. I promised Monica that John and Alexis...would be immune to this outbreak as well. Alexis...is the only other child that shares close similarities to William."

"All this time you strung me along, waiting for the right moment. Making me believe I had nothing left."

"I admit I enjoyed seeing you broken and defeated...as I said before. But if I didn't truely love you, Fox...I wouldn't have made everyone you care about immune to the apocalypse. Prices have to be paid somewhere."

To be continued...


	5. Chapter 5

Scully opened her eyes to a brightly lit room and instantly regretted it as she winced in pain. "Ah!"

"Hey, you're going to be okay," came a voice beside her. It wasn't Mulder's. It was similar, but younger and somewhat unadulterated by the harsh realities of life.

She turned and her eyes adjusted to better see the figure next to her. It was a tall, dark haired young man...a teenager, she guessed. "Who are you?"

He smiled. "I think you know the answer to that question."

"William?"

He responded with a nod. Scully looked at him, entirely at a loss for words. Obviously, she hadn't envisioned meeting him this way. Before she could respond or react, he walked to the opposite side of her bed, causing her to shift slightly. It was only then that she realized she was confined by the IV and various wires attached to her arms. Mulder was in the bed opposite her, but appeared to still be unconscious. "Mulder," she whispered, recalling that he had been near death.

William turned from Mulder to his birth mother. "He was very sick, but I was able to give him the stem cells he needed."

Scully gazed back at her partner. His complexion had made a vast improvement from when she saw him on the bridge. He was still pale, but he no longer looked near death. "William-I-" she felt the tears coming as she moved to remove the IV and devices attached to her arm.

"Dana," he started, moving back towards her. "You're extremely dehydrated, you need to stay here."

Scully took note of the long, slender arms pushing her back towards the bed. She sighed. She had so much she wanted to say, but couldn't find the words. "Is he going to be okay?" She managed.

William nodded. "He's dreaming though...I can tell," he said as he turned to note the way Mulder's body fidgeted uncomfortably. "I don't think it's good, but it's important we don't wake him until he's ready."

"Thank you," Scully said through tears. "You...you don't owe us anything. I can't thank you enough."

William managed a smile. "I've used my powers to do bad things...to hurt people. I want to do something good for a change."

Scully nodded, sitting back in the hospital bed. She wanted to ask him so many questions, but it would have to wait. "Where are we?"

"We're inside the ship."

Scully groaned as she felt her head throb. The spaceship she saw. Mulder said he had seen ones that were created by men. The ARVs.

"The virus," she said simply. "The world is ending."

Just as William could respond, Mulder shifted and winced as he opened his eyes to the brightly lit room.

"Mulder!" She gasped. She moved towards her partner's side as he woke. He reached for her and she took his right hand while placing her left on his cheek, willing him to look at her. "Oh God...oh God, Mulder."

He closed his eyes at the wonderful sight of his partner and then opened them again to look over at William. Mulder looked from Scully to William and then back to her with a question in his eyes. She nodded her response tearfully.

"We don't have much time. I stopped time so I could get to you both."

Scully looked at him skeptically.

Mulder groaned. He looked much better than before, but he was still recovering. "Stopped time? Now there's an X-File." It took him a moment to recall the dream he had. "Scully, the smoking man...Monica...she's," he groaned, trying to get out the words.

"It's okay, Mulder," Scully soothed.

"Yes...my grandfather, he's alive," William offered.

Scully looked back at her son. "William...where have you been all this time?"

He managed a small smile. "With Aunt Monica and Uncle John, but Aunt Monica had to ensure my safety by working with my grandfather. She's also..." William turned to Mulder. "Your sister...and I have a cousin named Alexis."

Mulder looked like a ghost. He closed his eyes and dropped his head back into the pillow.

Scully looked at William in shock. "But how...how can that be?"

"I'm sorry," he said. "I don't have time to explain. It would take hours. But we can reverse this outbreak."

"How?!" Scully asked.

"I'll need to reverse time...to before it begins. We have to change the future."

Was she dreaming? "Dad...Mulder will need to find the smoking man."

"But you?" Scully stated tearfully.

"You will find me again in time, but I won't be the same version of myself."

Scully was heartbroken. She had finally gotten to see her son after all these years.

"I want you to know one thing," he said.

"What?" Scully asked.

"You're going to have another baby."

Before he could continue, Scully laughed incredulously. "That's impossible. Even if it was possible, I'm in my fifties. There's no way I could-"

"I can't say when or give you any more details than that, but you will and it will be a miracle. For her sake, I hope we can change what's to come."

Scully was stunned and had no idea what to say. She didn't dare hope, yet tears welled in her eyes and she looked over at Mulder who had lost consciousness again.

"Oh and don't listen to the smoking man. He's a liar."

Suddenly, there was a flash of bright light and then nothingness.

-  
Mulder headed down to the office. He was late for work, but he had taken the time to stop and grab some coffee for Scully and himself. Things had been great this past week and he was happy they had made so much progress in finding their common language again. "Scully? I got us some coffee," he said as he walked into the office.

Just as he set the drinks down, he gasped in shock. Scully was behind the desk, laying on the floor unconscious. She had blood dripping down the side of her cheek.

"Shit. Scully? Scully?!"

He knelt down next to her to check her pulse. She was breathing, thank God.

Ignoring the screen of the computer with Tad O'Malley's site, Mulder grabbed the phone on his desk and dialed 911.

END

A/N: As you could tell the end scene left off at MSIII. I decided to wrap up some hiatus stories and figured this would be great to lead into ss11.


End file.
